3D-BioInfo services

Name Description ELIXIR Node

A very broad and active community of structural bioinformaticians exists across Europe. The structural Bioinformatics Community (3D-BioInfo) was officially created in May 2019. Our mission will be to better integrate protein structure-based data and tools across Europe, and to improve standardisation through better ontologies for the data and agreed benchmarking of methods. We will also strengthen the ties with the structural biology research communities in Europe and undertake dedicated educational, training and outreach efforts.

This project will focus on four main topics:

1. Infrastructure for FAIR structural and functional annotations

2. Standards and workflows for annotating and characterising biologically meaningful 3D structures of macromolecular assemblies

3. Biomacromolecule-ligand interactions

4. Tools to build and analyze Nucleic Acid structures: interoperability and FAIR data 

 ELIXIR UK, ELIXIR Czech Republic, EMBL-EBI, ELIXIR Belgium, ELIXIR Switzerland, ELIXIR Spain, ELIXIR Netherlands, ELIXIR Germany, ELIXIR Italy, ELIXIR Sweden, ELIXIR Norway, ELIXIR Finland, ELIXIR Denmark, ELIXIR Israel, ELIXIR France
ELIXIR Spain
ELIXIR Spain
ELIXIR Spain
ELIXIR Czech Republic
ELIXIR Spain
ELIXIR Spain
ELIXIR Spain
ELIXIR Spain
ELIXIR Czech Republic

This project addresses the limitations of current ontologies in capturing the dynamic nature of disordered protein regions by pursuing several primary objectives. Firstly, novel structural and functional ontologies will be developed to accurately represent the structural heterogeneity and dynamic functional annotations of proteins. These ontologies will incorporate timescales, annotating the kinetics of structural transformations to elucidate molecular mechanisms and regulatory pathways governing protein dynamics. 

Collaborating with existing databases and consortia will ensure seamless integration of ontological resources and experimental data, fostering interoperability and accelerating discoveries. A standardised file format specification will also be developed in collaboration with the Human Proteome Organisation Proteomics Standards Initiative, facilitating the encoding of structural state transitions within disordered protein regions. This specification will enhance data interoperability and exchange among research groups and databases, providing a common language for describing structural transitions and advancing our understanding of the functional implications of protein dynamics in biological systems.

 ELIXIR Belgium, ELIXIR Hungary, ELIXIR Italy, EMBL-EBI

This implementation study will create infrastructure to chart the experimentally sampled
conformational diversity of native proteins by exploiting data from the PDB, augmented with
results of state-of-the-art computational tools. By integrating resources/tools, workflows will be
developed to

i) Compare and cluster different conformations adopted by homologs of the same
protein,

ii) Identify protein regions with different flexibility properties.

Pipelines will be created to characterize conformational ensembles in terms of

i) The types of motions described (thermal fluctuations; collective motions),

ii) Their functional relevance, using sequence information and functional annotations.

These data will be integrated into the PDBe Knowledge Base and presented in the aggregated views (PDBe is an ELIXIR-Core-Data-Resource), which are freely available to the scientific community. Applications of these new capabilities will be explored in a joint gap analysis with the IDP and Proteomics Communities, including joint meetings, in order to identify future implementations that best serve ELIXIR goals.

 ELIXIR Norway, ELIXIR France, ELIXIR Spain, ELIXIR UK, EMBL-EBI, ELIXIR Belgium, ELIXIR Denmark, ELIXIR Hungary, ELIXIR Italy, ELIXIR Germany

Cellular and molecular biology are fundamental to ELIXIR's mission. As part of our 2024–28 Programme, we are committed to advancing data services and software for research on nucleic acids, proteins and other biomolecules. This initiative will address new demands for multi-omics and multi-modal analyses, including imaging, by developing methods and partnerships. We will also expand expertise in reusable data and software to incorporate FAIR models, ensuring robust solutions for modelling at all scales. 

The following projects are key to connecting the latest developments with established data resources, unlocking the potential of cellular and molecular biology:

 ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR France, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK, EMBL-EBI
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Ireland, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI

This project will increase interoperability between four ELIXIR resources (CATH, SWISS-MODEL, InterPro and PDBe), three of which are Core Resources, by building APIs that facilitate the import and export of data between them.

The ultimate goal is to improve provision of 3D-Models for protein domain sequences via CATH, SWISS-MODEL and InterPro. Less than 10% of known sequences have experimentally characterised 3D structural information and yet this data is often essential for understanding the protein’s molecular function and biological role and for determining whether residue mutations could damage the protein and lead to disease. So this integration is very timely as it will enhance links between sequence and structure data.

APIs will be built using well-established protocols and as well as promoting interoperability, and therefore sustainability, we will expand the data in each resource to ensure they serve a wider community of biologists.

 ELIXIR UK, ELIXIR Switzerland, EMBL-EBI

This project will increase interoperability between four ELIXIR resources (CATH, SWISS-MODEL, InterPro and PDBe), three of which are Core Resources, by building APIs that facilitate the import and export of data between them.

The ultimate goal is to improve provision of 3D-Models for protein domain sequences via CATH, SWISS-MODEL and InterPro. Less than 10% of known sequences have experimentally characterised 3D structural information and yet this data is often essential for understanding the protein’s molecular function and biological role and for determining whether residue mutations could damage the protein and lead to disease. So this integration is very timely as it will enhance links between sequence and structure data.

APIs will be built using well-established protocols and as well as promoting interoperability, and therefore sustainability, we will expand the data in each resource to ensure they serve a wider community of biologists.

 ELIXIR UK, ELIXIR Switzerland, EMBL-EBI
ELIXIR Spain
ELIXIR Spain